3 Years of my Life Spent Developing Image Processing Algorithms - Yours Free Open Source

Open Source Image Processing - Automated Analysis of Interfaces, Nano particles, Bubbles, and Electron Beam Effects in Liquid Cell Electron Microscopy

Our open source paper outlining the image processing algorithms we have developed over the last few years is live! The paper, code and sample videos are all available open source by the new Springer Open Journal Advanced Structural and Chemical ImagingWe maintain the code on GitHub, and have a screencast outlining the use of the algorithms on YouTube.


Automated analysis of evolving interfaces during in situ electron microscopy

Advanced Structural and Chemical Imaging 20162:2 DOI: 10.1186/s40679-016-0016-z
©  Schneider et al. 2016
Received: 15 November 2015
Accepted: 11 February 2016
Published: 26 February 2016


In situ electron microscopy allows one to monitor dynamical processes at high spatial and temporal resolution. This produces large quantities of data, and hence automated image processing algorithms are needed to extract useful quantitative measures of the observed phenomena. In this work, we outline an image processing workflow for the analysis of evolving interfaces imaged during liquid cell electron microscopy. As examples, we show metal electrodeposition at electrode surfaces; beam-induced nanocrystal formation and dissolution; and beam-induced bubble nucleation, growth, and migration. These experiments are used to demonstrate a fully automated workflow for the extraction of, among other things, interface position, roughness, lateral wavelength, local normal velocity, and the projected area of the evolving phase as functions of time. The relevant algorithms have been implemented in Mathematica and are available online.


Nicholas M Schneider

Nicholas M Schneider is a 2010 graduate from the Kate Gleason College of Engineering who is now a Doctoral Candidate at the University of Pennsylvania. Originally from an obscure town south of Buffalo, New York, he attended the Rochester Institute of Technology where he received concurrent Bachelor of Science and Master of Science degrees. While there he had a number of Co-ops including a six month stay as a Design Engineer at Lockheed Martin and Research positions with Dr. Satish Kandlikar. Nicholas currently works with Dr. Haim H Bau in the field dubbed “in situ electron microscopy of liquid systems” where he studies applications in energy and biological systems. Outside of the lab, Nicholas Schneider is a Graduate Associate in Rodin College House and enjoys running (he ran his second Philly Marathon this past November), cooking, baking, reading, and justifying his coffee addiction by making it a hobby.